minerva (16.0.0~beta.2) stable; urgency=medium * Bug fix: correct background order for old projects restored (#1533) * Bug fix: search chemicals by target returned chemicals not bounded by disease (#1535) * Bug fix: problem with export map with submaps fixed (#1540) * Bug fix: removing user removed backgrounds in projects created by user (#1527) * Bug fix: removing background did not remove images from server (#1526) -- Piotr Gawron Fri, 3 Sep 2021 11:00:00 +0200 minerva (16.0.0~beta.1) stable; urgency=medium * Backward incompatibility: layout parameter in minerva url is not supported anymore * Small improvement: info about background and data overlays is separated in edit project panel (#1515) * Bug fix: there was issue with updating data overlay in admin panel "Unknown parameter: defaultOverlay" (#1489) * Bug fix: data overlays uploaded in complex map were not processed properly (#1485) * Bug fix: sort of the overlays in General Overlays in the left panel was wrong (#1486) * Bug fix: overlay owner must be defined (#1488) * Bug fix: there was issue when upgrading backgrounds in admin panel (#1514) * Bug fix: there was issue when editing and saving data overlay (#1494) * Bug fix: problem with adding comments (#1495) * Bug fix: project with invalid data might cause problem on create/update/delete (#1509) * Bug fix: exporting part of map as image caused removing not drawn species from the database (#1508) * Bug fix: adding user with already existing login and changing his privileges occured with error (#1507) * Bug fix: export model as model could cause an issue (#1500, #1502) * Bug fix: problem with export as image with data overlays (#1503, #1498, #1496) * Bug fix: chrome autofill is disabled for "Search: " in admin panel tables * Bug fix: top map was not selected properly sometimes (#1487) * Bug fix: data overlays in comlex upload prevented error to be propagated to user (#1499) * Bug fix: searching for all chemicals by target did not work (#1490) * Bug fix: searching by chemical/drug/mirna in left panel focus the proper tab in the InfoWindow (#1492) * Bug fix: search tab becomes active when drug/chemical/mirna result are available (#1491) -- Piotr Gawron Fri, 25 Jun 2021 08:00:00 +0200 minerva (16.0.0~beta.0) stable; urgency=medium * Backward incompatibility: debian package cannot be upgraded from version prior to 12.1.0 (#1464) * Small improvement: artifitial source and sink is created separately for each uncomplete reaction (#1475) * Small improvement: homomultimer information is provided in API (#1468) * Small improvement: missing info about species for SBML parsing warning (#1472) * Small improvement: information about dimer in sbgn is provided only once if the information is duplicated in sbgn data (#1358) * Small improvement: glyph quality is improved (#1458) * Small improvement: search results are group by diagram (#1451) * Small improvement: "Failed to fetch" errors are reported in a way that suggest retrying before submitting error report (#738) * Small improvement: reverse search pop-up reorganized (#1366) * Bug fix: arrows without a "process" box had an irregular empty space in their lines (#1471) * Bug fix: when selecting drug in the alias window the input text is updated (#1365) * Bug fix: zoom slider was not updated when clicking on +/- in genome browser (#1064) * Bug fix: there was no possibility to see gene variants (regression 16.0.0~alpha.1) -- Piotr Gawron Fri, 30 Apr 2021 16:30:00 +0200 minerva (16.0.0~alpha.1) stable; urgency=medium * Backward incompatibility: deprecated columns in data overlays are no longer supported (#958) * Backward incompatibility: comment does not contain name anymore (#1070) * Backward incompatibility: publication pagination API slightly changed (#1007) * Backward incompatibility: elements in data overlay are returned differently when using data overlay API (#1007) * Improvement: performance improved - map is available immediatelly after tomcat starts (#1007) * Improvement: minerva does not require huge amounts of memory anymore (#1007) * Improvement: data overlay allows for multiple hits per element (#1007) * Small improvement: "dbSNP", "IMGT HLA", "PMC", "Complex Portal" identifiers are supported (#1452, #1450, #1420) * Small improvement: information about perfect search are stored in the url (#1376) * Small improvement: context menu exporting map is more precise about scope (#1447) * Small improvement: styling of GENERIC search tab title improved (#1364) * Small improvement: SBML render contains information about species shapes (#1055) * Small improvement: SBML render contains information about modification residues (#1456) * Small improvement: SBML render contains information about structural states (#1456) * Small improvement: SBML render contains process rectangle for reactions (#1457) * Bug fix: refreshing page after removing last project on the page redirect to proper page (#1051) * Bug fix: removing plugin that does not exist anymore does not raise an error (#1289) * Bug fix: broken overlays crashed minerva upgrade (#1453) -- Piotr Gawron Fri, 19 Mar 2021 10:00:00 +0200 minerva (16.0.0~alpha.0) stable; urgency=medium * Backward incompatibility: deprecated columns in data overlay table are no longer supported: reverseReaction, reaction_identifier, reactionIdentifier, reference_genome_type, reference_genome_version, allel_frequency, lineWidth, elementIdentifier, references, model_name (#958) * Backward incompatibility: information about old search queries removed from database (it can be still accessed using proper log managing) * Improvement: automatically generated API documentation available in the package (#1016) * Bug fix: md5 hash function of plugin was not computed properly * Bug fix: exported gpml for every compartment contained list of species name in the comment section -- Piotr Gawron Thu, 27 Aug 2020 13:00:00 +0200 minerva (15.1.4) stable; urgency=medium * Bug fix: structural state information data was not available for complexes (#1476) * Bug fix: orthogonal reactions to phenotypes from CellDesigner were drawn incorrectly (#1454) * Bug fix: orthogonal reactions to drugs from CellDesigner were drawn incorrectly (#1454) -- Piotr Gawron Tue, 30 Apr 2021 18:00:00 +0200 minerva (15.1.3) stable; urgency=medium * Bug fix: modifier reactions to phenotype were incorrectly translated to Process Description reactions when exporting to SBGN-ML (#1445) * Bug fix: AND/OR text was missing when drawing diagram as SBGN (#1428) * Bug fix: annotators details changes were not saved in few consecutive updates (#1446) * Bug fix: SearchListener was not triggered when clicking on highlighted elements (#1449) -- Piotr Gawron Tue, 9 Feb 2021 09:00:00 +0200 minerva (15.1.2) stable; urgency=medium * Bug fix: automatic annotations are sometimes missing after project upload (#1434) * Bug fix: export to SBML failed if reactant/product line had length=0 * Bug fix: downloading submap from big project as a map quite often resulted in error (#1440) * Bug fix: colors for values in exported image were incorrect for intermediate values, like 0.5 (#1442) * Bug fix: when there is a problem with updating sorting preferences no error is raised but silent warning is reported in the console (#1426) -- Piotr Gawron Mon, 11 Jan 2021 12:00:00 +0200 minerva (15.1.1) stable; urgency=medium * Bug fix: export to CD maps with species containing ":" or "." in species id generated files that could not be opened in CellDesigner (#1363) * Bug fix: zoom level change was not reflected in the url when submap was opened (#1338) * Bug fix: API call returning list of overlays returned for non existing project returned access denied status insted Not Found (#1370) * Bug fix: results for chembl targetting uniprot without gene name (for example P0C2L1) could crash caching (#1377) * Bug fix: removing non-existing project results in warning not an error message (#1367) * Bug fix: opening map in google maps without background resulted in unexpected error (#1416) * Bug fix: normal user could not update tos information (#1419) * Bug fix: and operator in SBGN-like view was not drawn (#1408) * Bug fix: export of overlayed map as an image did not respect overlay colors (#1417) -- Piotr Gawron Thu, 23 Nov 2020 15:00:00 +0200 minerva (15.1.0) stable; urgency=medium * Small improvement: information if species has activity, hypothetical flag set is available over REST API for element (#1379) * Small improvement: "Human Disease Ontology", "IUPHAR ligand" and "Protein Modification Ontology" annotation types are handled (#1359) * Small improvement: annotations are exported in SBGN extension that can be opened by newt (#1296) * Small improvement: plugin API allows to add/remove data overlays (#1153) * Small improvement: logged user can change password (#1119) * Small improvement: possibility to reset password added (#275) * Small improvement: import SBML uses render:fill color for compartment (#1254) * Small improvement: in SBML render stroke color for glyphs is used for defining font color * Small improvement: when SBML with layout contains different glyph text and species name those two values are assigned to name and full name (#1275) * Small improvement: process rectangle can be specified in SBML with reaction bounding box (#1292) * Small improvement: API allows to remove plugin data entry (#1298) * Small improvement: transport/translation/transcription reactions are exported to SBGN PD (#1302) * Small improvement: Unknown Transition Reaction is exported to GPML as CONVERSION (#1300) * Small improvement: when uploading complex map with images warnings are raised if images are not referenced in coords.txt file (#1308) * Small improvement: hitting enter after filling credentials automatically tries to log in (#1312) * Small improvement: rest API provides information about element glyph and z index * Small improvement: pathways with glyphs and z index below 0 are not clickable (#1314) * Small improvement: Modifier Reaction from CellDesigner are exported properly to SBGN-ML PD (#1320) * Small improvement: SBGN notes are imported properly (#1319) * Small improvement: SBGN notes are exported properly (#1319) * Small improvement: possibility to customize request account email title (#1330) * Bug fix: SBML text labels that were referencing layout aliases using layout:graphicalObject attribute were not handled properly (#1356) * Bug fix: MolArt version upgraded to handle new protein API syntax (#1399) * Bug fix: LDAP connection did not work properly where uid in LDAP/AD contained upper case letters (#1404) * Bug fix: miriam urls in new format (like: https://identifiers.org/kegg.compound:197020) are parsed properly for all know identifier types (#1359) * Bug fix: in SBGN-like view protein state should be drawn as stadium-shape (#1357) * Bug fix: export to image from selected polygon contained all elements inside rectangle bounded by the polygon coordinates (#1096) * Bug fix: continuous refreshing list of project when uploading/removing project did not allow to change other project details (#996) * Bug fix: when multi extension did not contain species type list import of SBML crashed * Bug fix: when content of element popover is too wide the scrollbar is visible (#1269) * Bug fix: problem with accessing mirtarbase data on new instances fixed -- Piotr Gawron Thu, 22 Oct 2020 15:00:00 +0200 minerva (15.0.3) stable; urgency=medium * Bug fix: caching chemicals/drug data on big map could cause Out of Memory issues (#1315) * Bug fix: when there is a problem with minerva deployment on tomcat proper warning message is presented in admin panel (#1332) * Bug fix: API call updating user preferences did not handle properly conflicts on new gui properties (#1326) * Bug fix: "bqbiol:hasTaxon" relation type is not supported by CellDedigner and is now transformed during export into something readable by CellDesigner (#1281) * Bug fix: concurrency issue that could happen rarely on first search of the map and put the project into "unsearchable" state is fixed (#1333) * Bug fix: when edit project buton was clicked on project that was removed in another tab there was an error thrown (#1343) * Bug fix: chebi and entrez annotations were incorrectly exported to GPML (#1349) * Bug fix: exporting to GPML sometimes resulted in invalid modification point end for catalysis (#1350) * Bug fix: elements name were not escaped properly when exporting to GPML (#1351) * Bug fix: reaction with description and pubmed reference was incorrectly exported to GPML (#1352) -- Piotr Gawron Thu, 13 Aug 2020 15:00:00 +0200 minerva (15.0.2) stable; urgency=medium * Bug fix: annotations using identifiers.org urls sometimes required http and sometimes required https url (#1297) * Bug fix: map notes were not exported to GPML * Bug fix: reaction notes were not imported from GPML * Bug fix: export of notes could create invalid GPML file (#1299) * Bug fix: there was an issue with exporting color and line type of reaction additional reactant/product (#1303) * Bug fix: coordinates of children in compact complexes in CellDesigner were wrong (#1304) * Bug fix: user data overlays were not removed when user was deleted (#1301) * Bug fix: kinetic parameters exported to SBML created invalid SBML file (#1305) * Bug fix: text area were not converted to GPML using conversion API (#1306) * Bug fix: name provided by user in comment dialog was not visible in admin panel (#1245) * Bug fix: bqmodel:isInstanceOf and bqmodel:hasInstance relation types were not handled properly (#1281) * Bug fix: "bqmodel:isInstanceOf", "bqmodel:hasInstance", "bqbiol:hasProperty", "bqbiol:isPropertyOf" relation types are not supported by CellDedigner and are now transformed during export into something readable by CellDesigner (#1281) * Bug fix: at random time points there was an issue with cached data (#1323) * Bug fix: connection to DAPI timeouted sometimes which resulted in error when checking for all chemicals for specfific protein (#1324) * Bug fix: complex/compartment with empty name was incorrectly exported to CellDesigner (#1310) -- Piotr Gawron Wed, 1 Jul 2020 16:00:00 +0200 minerva (15.0.1) stable; urgency=medium * Bug fix: when there was problem with DAPI minerva threw unexpected error (#1316) * Bug fix: DAPI connection must go over HTTPS (#1316) -- Piotr Gawron Fri, 26 Jun 2020 11:00:00 +0200 minerva (15.0.0) stable; urgency=medium * Backward incompatible: old connection to CTD is removed and replaced with new Data-API interface that closely check license compliance * Backward incompatible: old connection to DrugBank is removed and replaced with new Data-API interface that closely check license compliance * Backward incompatible: some custom fields (like transparency zoom level) are not exported to CellDesigner file (#1071) * Backward incompatible: truncation/association/dissociation points are represented as a dot in all new images/uploaded maps (#1265) * Backward incompatible: and/split points are represented as a dot in all new images/uploaded maps (#1253) * Backward incompatible: reaction will be on top of elements in maps uploaded from formats that does not contain z-index (#1251) * Backward incompatible: when uploading complex map with submap there is no possibility to change submap name (#947) * Improvement: logs provided for validation data model are structured (#325) * Improvement: import/export of GPML implemented * Improvement: API allows to merge files (#1208) * Improvement: export to SBGN/SBML/GPML format provides popup with list of warnings occurred in the translation process (#713) * Improvement: support for rendering colors in SBGNML added (#1009) * Small improvement: compartments in not layouted SBML file are more scattered (#326) * Small improvement: when downloading a map results in too big file (>1MB) the content is compressed and returned as a zip file (#348) * Small improvement: confirmation dialog when removing "general view" overlays contain proper warning (#809) * Small improvement: CellDesigner text area object can have "BorderColor" property defined (#806) * Small improvement: list of submaps is sorted alphabetically (#962) * Small improvement: notification about new releases of minerva added in admin panel (#961) * Small improvement: font awesome upgraded to 5.1 (new icon styles) * Small improvement: header contains login/logout button and access admin panel button (#982) * Small improvement: autocomplete for chemical searches is enabled (#841) * Small improvement: "bqbiol:occursIn" and "bqmodel:isDerivedFrom" and handled in annotations (#1190), * Small improvement: 3DMET, Evidence Code Ontology, Kegg Glycan, LipidBank, Chemical Component Dictionary annotations are supported (#1190) * Small improvement: SWISS-model annotations are supported (#1249), * Small Improvement: SBO annotation support added (#1194) * Small improvement: support for annotations added: ChemIDplus, EcoGene, FlyBase, GeneDB, Intact, Kegg Drug, KNApSAcK, LIPID MAPS, NCBI Protein, PATO, RGD, SPIKE, TTD Drug, ZFIN BioEntity * Small Improvement: additional annotation uri qualifiers added: hasProperty, isPropertyOf (#1193) * Small improvement: small css improvement in info tab (#1104) * Small improvement: import/export to SBML of unit of information obtained from SBGN source is supported (#1088) * Small improvement: rounded rectangle is used to visualize Simple chemicals in SBGN-like view according to the newest SBGN specification (#1094) * Small improvement: after removing project is confirmed the system enforce waiting until remove status is confirmed (#1106) * Small improvement: when typing drug, list of autocomplete drugs should be available limited to the drugs that target something on the map (#641) * Small improvement: data not compliant with database constraints (for instance too long species identifiers) will be automatically adjust instead of crashing project upload (#1041) * Small improvement: reaction lines in SBML files without layout are set outside of the species (not in the center, #1023) * Small improvement: sort order of tables in admin panel is preserved among sessions (#836) * Small improvement: simple molecules in SBGN compliant view are drawn as ellipses not circles (#796) * Small improvement: uploaded map is automatically cached (#983) * Small improvement: molart updated to version 1.5.0: Ability to show unobserved structure regions in the sequence view. * Small improvement: list of genomes is automatically refreshed during genome upload (#820) * Small improvement: items in context menu are reorganized (#787) * Small improvement: CellDesigner files from version 2.5 should be parseable * Small improvement: plugins in admin panel can be revalidated to update info about the plugins (name, version) * Small improvement: there is possibility to define default plugins loaded with every opening of a map (#967) * Bug fix: pathways are visualized in image converter (#1266) * Bug fix: conversion of file containing BOM did not work (#1264) * Bug fix: proper color is parsed from CellDesigner species marked as 'brief' * Bug fix: upload of SBGN files didn't process unicode characters properly when server was running with encoding different than UTF-8 (#1142) * Bug fix: kinetic equation in reaction that referenced complex (instead of target species) crashed CellDesigner upload (#1212) * Bug fix: kinetic equation in SBML that used speciesReference id crashed upload (#1190) * Bug fix: layout reaction with duplicated reaction element crashed SBML upload (#1190) * Bug fix: conversion from SBML to CellDesigner escaped "<" twice (#1228) * Bug fix: Select annotation dialog width is at least 840px (#1210) * Bug fix: modifiers joined by operator were exported to SBML without line corresponding to the operator (#1199) * Bug fix: first state variable that does not match modification residue is translated to structural state when importing from SBGNML (#1088) * Bug fix: exported SBML was not compliant with the standard when element name was empty (#1147) * Bug fix: invalid data overlays in uploaded zip file created "valid" project that could not be opened (#1086) * Bug fix: cardinality in SBGN-like view is drawn in separate unit (#1157) * Bug fix: notes from SBML are parsed with all html tags (#1196) * Bug fix: converter API append conversion warnings to generated output notes * Bug fix: newt use incorrect attributes when exporting render information that could not be parsed by minerva (#1127) * Bug fix: catalysis to protein was not parsed from SBGN file (#1116) * Bug fix: antisenseRNA shape is inferred from SBGN when antisenseRNA text is present in glyph label (#1114) * Bug fix: export to SBGN sometimes crashed due to concurrency issues (#1126) * Bug fix: CellDesigner models where start and end point of reaction was the same were not handled properly (#1131) * Bug fix: more than one authors in CellDesigner file were not parsed properly (#1156) * Bug fix: SBGN reaction with no reactants crashed map upload (#1148) * Bug fix: import from SBGN assigned invalid name to species that didn't have label defined (#1093) * Bug fix: drawing protein in SBGN-like style didn't handle properly dimension of the species for multimers bigger than 2 (#1091) * Bug fix: drawing of structural state in SBGN-like style uses RoundedRectangle instead of Ellipse which was not SBGN-compliant (#1095) * Bug fix: import from CellDesigner rounded alias dimension to integer * Bug fix: compartments limited by corner (left-top corner compartment, etc) are parsed properly from CellDesigner files * Bug fix: structural states of proteins are imported properly from SBGNML PD (#995) * Bug fix: export to CellDesigner names with new line is properly handled (#930) * Bug fix: layout of the exported reactome pathways is fixed when reactome exporter violates SBGN specification (#707) * Bug fix: unknown catalysis boolean gate modifiers in CellDesigner are visualized with proper line type across all included modifiers (#957) * Bug fix: dimension of the modifications is the same as in minerva when exporting to SBGNML-PD (#554) * Bug fix: position of structural state is preserved on upload CellDesigner file (#671) * Bug fix: problematic notes doesn't crash CellDesigner upload (#968) -- Piotr Gawron Mon, 22 Jun 2020 11:00:00 +0200 minerva (14.0.13) stable; urgency=medium * Bug fix: chrome modified default css and service looked ugly in chrome (#1260) * Bug fix: uploaded HGNC identifiers that looks like "HGNC:HGNC:1234" are changed to "HGNC:1234" (#1252) * Bug fix: creating comment with too long name/email resulted in Internal Server Error - now the proper error message is returned (#1245) * Bug fix: user cannot put too long name in a comment dialog (#1245) * Bug fix: when url contained invalid submap id unhandled error was raised (#1243) -- Piotr Gawron Wed, 3 Jun 2020 17:00:00 +0200 minerva (14.0.12) stable; urgency=medium * Bug fix: comments on submaps were not visible (#1230) * Bug fix: removing comment from submap did not work * Bug fix: reaction name containing "<" character was exported inproperly to CellDesigner (#1227) * Bug fix: doi annotation was inproperly parsed from CellDesigner file and resulted in not clickable link (#1231) * Bug fix: when plugin data was too big 500 error was returned (#1232) * Bug fix: removing plugin in admin panel removes it from server permanently (#1211) -- Piotr Gawron Mon, 11 May 2020 17:00:00 +0200 minerva (14.0.11) stable; urgency=medium * Bug fix: complex with no border was inproperly imported from CellDesigner (#1198) * Bug fix: export to CellDesigner deal with CellDesigner issue that does not allow compartment species alias to be shorter than 2 characters (#1204) * Bug fix: kinetic parameters with INFINITY values could not be uploaded to minerva (#1202) * Bug fix: infinity value in kinetic parameter could not be parsed from CellDesigner file minerva (#1203) * Bug fix: author list inproperly presented author data when some fields were missing (#1201) * Bug fix: refreshing minerva page with more than one plugin opened might led to an error due to race condition (#1197) -- Piotr Gawron Mon, 31 Mar 2020 09:00:00 +0200 minerva (14.0.10) stable; urgency=medium * Bug fix: reaction without ports in SBGN crashed upload (#1065) * Bug fix: annotations using newer identifiers.org uri schema were truncated by one character (#1191) * Bug fix: long annotation string broke listing of annotations (#1155) -- Piotr Gawron Mon, 16 Mar 2020 14:00:00 +0200 minerva (14.0.9) stable; urgency=medium * Bug fix: simultanous export to SBML of more than one file could result in 500 Internal Server Error (#1110) * Bug fix: refresh data overlay did not hide data overlays that were removed and selected (#1097) * Bug fix: transparent complexes are shown with wrong color (#1103) * Bug fix: CellDesigner sometimes marked reduced notation reaction as reversible even though they were not visualized so (#1109) * Bug fix: when data overlay was being removed user could request to remove overlay second time and an error was thrown (#1121) * Bug fix: when data overlay name in zip uploaded zip file is not present the name of a file is used as overlay name (#1065) * Bug fix: uploading empty data overlay resulted in an error (#1123) * Bug fix: exporting map with glyphs crashed (#1130) * Bug fix: transcription factor on black&white gene are drawn in black (#1132) * Bug fix: when SBGN file contained consumption starting in process minerva crashed (#1063) * Bug fix: when SBGN file contained reaction where every node started in the same process port minerva crashed crashed (#1063) * Bug fix: activity flow reaction inside SBGN PD caused upload of map to crash * Bug fix: reaction without product in SBGN crashed upload of map * Bug fix: when SBGN production pointed directly to process instead of process port upload crashed * Bug fix: handle properly corrupted cached chembl drug data (#1140) -- Piotr Gawron Tue, 25 Feb 2020 15:00:00 +0200 minerva (14.0.8) stable; urgency=medium * Bug fix: API didn't allow to upload plugins with local url (#1084, regression 14.0.7) * Bug fix: upload of data overlay with two entries having different uniprot identifier but pointing to the same gene crashed (#1083) * Bug fix: don't allow to remove plugin twice (#1081) * Bug fix: upload of SBML file with very short reaction length could produce a map that couldn't be exported to SBML anymore (#1078) * Bug fix: import of structural state from SBGN-ML PD that cannot be normalized to residue is changed into structural state without losing information (#1062) * Bug fix: import of stimulation modifiers from SBGN-ML crashed converter (#1063) * Bug fix: export to SBGN files created from newt source produced corrupted disconnected reactions * Bug fix: upload from zip file allowed empty overlay name (#1065) * Bug fix: genome browser slider didn't work properly in Safari on non-default Browser zoom level (#1048) * Bug fix: project without background overlay but with some custom data overlays crashed with an error (#1066) * Bug fix: when session expires updating options in configuration panel threw unhandled error (#1068) -- Piotr Gawron Tue, 28 Jan 2020 11:00:00 +0200 minerva (14.0.7) stable; urgency=high * Bug fix: API allowed to provide malformed plugin url that could be used for xss attack (#1073) -- Piotr Gawron Tue, 14 Jan 2020 17:00:00 +0200 minerva (14.0.6) stable; urgency=medium * Bug fix: opening map with no background overlays and search request in url provides proper error message (#1046) * Bug fix: search by identifier didn't consider identifiers added by annotators (#1047) * Bug fix: if map has SHOW OVERVIEW, the legend/comment/clear were not displayed at all (regresion 14.0.5, #1045) * Bug fix: when there is a problem with database during removing project, project removal doesn't hang (#1058) * Bug fix: coloring of the reaction wasn't applied to center of reaction (regression 14.0.0, #1057) * Bug fix: genetic variant overlay improperly processed elements identified by miriam identifiers, like uniprot (#1059) * Bug fix: invalid information was provided for genetic variants overlay when map organism was defined (#1060) -- Piotr Gawron Wed, 19 Dec 2019 13:00:00 +0200 minerva (14.0.5) stable; urgency=medium * Bug fix: copy-paste of genetic-variant data overlay into Add overlay content dialog could crash upload (#1040) * Bug fix: some annotators (like Cazy) were crashing on old installations (#1029) * Bug fix: uploading a map that breaks postgres constraints hung upload of the project (#1028) * Bug fix: uploading of the page with low internet connection speed could produce empty screen for several seconds/minutes - now the loading icon is present (#1025) * Bug fix: search for NADH drug resulted in drug with empty name (#1018) * Bug fix: export to SBML didn't handle properly arrows (#1015) * Bug fix: Font colour of text area was preserved in Empty view (#1014) * Bug fix: exported sbml file always contain model identifier (#1013) * Bug fix: typo allel reverted to allele in overlay data (regression 14.0.0, #1012) * Bug fix: after loading/removing too many plugins it was impossible to load new plugins (#1011) * Bug fix: CLEAR button disappears after legend, comment checkboxes when plugin tab used to much space (#976) -- Piotr Gawron Tue, 03 Dec 2019 12:00:00 +0200 minerva (14.0.4) stable; urgency=high * Bug fix: some SBGN files uploaded to minerva could not be exported to SBML due to problems with identifiers used by SBGN (#1006) * Bug fix: upload of data overlay with conflicting overlay types caused error (#998) * Bug fix: upload of sbml file with protein modifications inside complex crashed visualization (#966) * Bug fix: list of overlays for admin and curator included also other people overlays (regression 14.0.3, #1008) * Bug fix: refresh button did not refresh overlay list after overlay was removed over API (#997) -- Piotr Gawron Thu, 07 Nov 2019 11:00:00 +0200 minerva (14.0.3) stable; urgency=medium * Bug fix: default zoom level on main map works even when x or y are undefined (#993) * Bug fix: sbml parser had sometimes problems with combining layout and multi packages (#966) * Bug fix: parsing of CellDesigner files that contained substanceUnits could crash the upload (#985) * Bug fix: verification of version length added when uploading project implemented (#978) * Bug fix: CLEAR button disappeared when plugin tab used to much space (#976) * Bug fix: removing data overlay refreshes list of overlays in info window (#974) * Bug fix: general overlays are always on top of data overlays in info window (#975) * Bug fix: refresh button in overlay panel synchronise list of general and user provided data overlays (#975) * Bug fix: changing order of data overlays is reflected in info window * Bug fix: opening map with no available background crashed (#964) * Bug fix: uploading SBGN file that does not pass xsd validation provides a warning, but does not fail upload (#937) * Bug fix: export of the map to SBML that was imported with older version (below 14.0.0) didn't produce valid SBML (#970) * Bug fix: fields in add project window are reinitialized after each open (#963) * Bug fix: filename case in uploaded zip files is preserved (#964) * Bug fix: +/- buttons were misaligned in genome browser (#942) * Bug fix: color of links in the left panel was unintentionally changed (#990) * Bug fix: minerva logo in left panel is centred properly * Bug fix: width of search button icon was too big -- Piotr Gawron Wed, 18 Oct 2019 15:00:00 +0200 minerva (14.0.2) stable; urgency=medium * Bug fix: Genetic data overlay uploaded prior to 14.0.0 crashed maps (#988) -- Piotr Gawron Wed, 15 Oct 2019 11:00:00 +0200 minerva (14.0.1) stable; urgency=medium * Bug fix: maps that were annotated using old Biocompendium annotator could not load properly (#986) -- Piotr Gawron Wed, 15 Oct 2019 9:00:00 +0200 minerva (14.0.0) stable; urgency=medium * Feature removal: BioCompendium annotator removed (#32) * Feature removal: support for tomcat7 removed (#828) * Feature: security layer redesigned - privilege types and scope changed (#636, #624) * Feature: log4j is replaced with log4j2 logging mechanism (#291) * Feature: database installed via debian package is done via dbconfig-commons (#469) * Feature: Replaced connection pool manager C3P0 with better maintained Hikari - restart of postgresql database doesn't require restart of tomcat (#564) * Small improvement: debian package can be installed on debian:buster (#879) * Small improvement: info window contains information about overlay No (#919) * Small improvement: sorting by columns that doesn't make sense in admin panel is disabled (#895) * Small improvement: version of minerva is visible in map browser panel * Small improvement: small info about annotator details is available in select annotators dialog (#923) * Small improvement: CellDesigner layers are always visualized as pathways (#813) * Small improvement: notification email uses minerva name and id of affected project (#926) * Small improvement: information about person who uploaded project is visible in list of projects (#927) * Small improvement: tab with list of glyphs is available when adding project with glyphs (#925) * Small improvement: BackgroundColor parameter should be assigned using ":" character (#929) * Small improvement: anonymous login is no longer required - each API query outside session is authorized with anonymous user privileges (#629) * Small improvement: bcrypt is used for password encryption (#387) * Small improvement: caching is active by default for new users when uploading project (#202) * Small improvement: when removing overlay in admin panel there is a confirmation dialog (#696) * Small improvement: overlay name is obligatory (#698) * Small improvement: list of projects in admin panel contains creation date (#447) * Small improvement: links in list of publications open in new tab (#447) * Small improvement: target gene in search panel contains also information about type of database that identifies the target (#66) * Small improvement: redundant 'references' field in gene variants data overlay is now deprecated (#850) * Small improvement: information about deprecated columns in data overlay is visible in overlay list (#838) * Small improvement: publication list is resizeable (#740) * Small improvement: user list on project edit dialog is sortable (#808) * Bug fix: exported SBML passes online validation (#831) * Bug fix: allow user to remove own comments (#931) * Bug fix: validation of project name length is provided (#950) * Bug fix: list of "Copy from" elements in "Select valid annotations" dialog is shortened to used bio entity types (#911) * Bug fix: version of the project is limited to 20 characters (#951) * Bug fix: export to CD could misalign reaction lines that were imported from format that didn't require reaction line to be attached to the species (#933) * Bug fix: problem with uploading data_overlays with type included in header (#936) * Bug fix: work on FF Private Window mode could cause logout or raise an error on when opening new tab with minerva (#892) * Bug fix: fetching list of miRnas resulted sometimes in "Internal Server Error" (#889) * Bug fix: edit project dialog verifies organism id (#914) * Bug fix: all colors in boolean reaction (from CellDesigner) are processed properly (#907) * Bug fix: proper line type for boolean reaction is used on the whole reaction (#908) * Bug fix: creating project with too long name hung upload (#916) * Bug fix: too long user login threw an error (#915) * Bug fix: when uploading generic data overlay the type was not updated in case the type was not specified in the input file (#906) * Bug fix: list of types when copying from annotators contains only types that are selectable in the dialog (#911) * Bug fix: too long name for data overlay in info window is trimmed (#919) * Bug fix: too long name in general overlay list is wrapped (#857) * Bug fix: after genome is removed list of genomes is refreshed (#922) * Bug fix: REST API bioEntities:search method didn't limit results to the submodel id (#860) * Bug fix: Empty Overlay colours were not preserved during export to CellDesigner (#714) * Bug fix: problem with unloading plugin is properly handled (#884) * Bug fix: upload of invalid plugin doesn't add it to plugin tab and list of loaded plugins (#885) * Bug fix: export to CellDesigner of reaction with two modifiers connected with boolean operator resulted was skipping some layout information * Bug fix: reaction in SBGNML file containing two products was improperly drawn * Bug fix: color handling in CellDesigner did not work properly for modifiers inside boolean gateway * Bug fix: CellDesigner file exported from minerva was not fully compliant with SBML standard (#831) * Bug fix: MiRNA targets are limited only to the organism associated with the map (#66) * Bug fix: Search drug by target element did not return values when this element was annotated automatically (#216) -- Piotr Gawron Wed, 09 Oct 2019 12:00:00 +0200 minerva (13.2.0) stable; urgency=medium * Small improvement: MolArt v1.4 is used which provide information from PredictProtein (#913) * Bug fix: search by drugs didn't check synonyms in chembl database * Bug fix: verification of overlay type added (#917) * Bug fix: opening edit project/user dialog returned list of users/projects to the 1st page (#909) * Bug fix: show element title option wasn't influencing title visibility (#910) -- Piotr Gawron Thu, 29 Aug 2019 17:00:00 +0200 minerva (13.1.3) stable; urgency=medium * Bug fix: refreshing list of projects or list of users doesn't change active page (#870) * Bug fix: submap list must be selected to export from every submap (#874) * Bug fix: export map as image properly uses bottom limit (#875) * Bug fix: reaction info window wasn't closed on CLEAR (#876) * Bug fix: name of the uploaded file is displayed when adding overlay (#849) -- Piotr Gawron Wed, 14 Aug 2019 17:00:00 +0200 minerva (13.1.2) stable; urgency=medium * Bug fix: Information about problematic zip file is more specific (#865) * Bug fix: Url didn't contain list of opened plugins and they weren't reload automatically on refresh (#866) -- Piotr Gawron Mon, 22 Jul 2019 17:00:00 +0200 minerva (13.1.1) stable; urgency=medium * Bug fix: adding gene mapping before the genome caused an error (#835) * Bug fix: "Terms of Use" change to "Terms of Service" in all places (#843) * Bug fix: upgrade to 13.1.0 crashed on machines where every element was inside compartment (#856) * Bug fix: searching for some drugs in chembl didn't provide any results even though that data exists, for instance 'DORLIMOMAB ARITOX' (#842) * Bug fix: user wasn't logged out in all tabs when the log out event appeard in only one of them (#847) -- Piotr Gawron Tue, 2 Jul 2019 19:00:00 +0200 minerva (13.1.0) stable; urgency=medium * Feature: annotators are more flexible - you can define set of input and outputs used by annotator (#617) * Feature: changes in admin panel doesn't require saving - they are saved automatically (#676) * Feature: elements can have custom glyphs used for visualization (#487) * Small improvement: model_name renamed to map_name in data overlay columns (#827) * Small improvement: name, type, reference_genome_type and reference_genome_version column in genetic variant data overlay are deprecated (#827) * Small improvement: all bio entities have z-index associated with them (#487) * Small improvement: validation of the organism and disease id on map upload added (#618) * Small improvement: added current username next to logout button in admin panel (#660) * Small improvement: New comment dialog does not contain content of previous comment dialog (#680) * Small improvement: Left logo is configurable (#731) * Small improvement: list of element types in choose annotator dialog is sorted (#798) * Small improvement: Plugin API provides list of overview images (#702) * Small improvement: Plugin API allows to show/hide overview images (#702) * Small improvement: Plugin API allows to trigger search on the map (#702) * Small improvement: Plugin API allows to clear search results on map (#702) * Small improvement: edit/remove project button is disabled until project is uploaded (#683) * Small improvement: warning about capslock is visible on login page when necessary (#658) * Small improvement: names of columns in data overlay are unified: no whitespace, "_" used as separator (#596) * Small improvement: list of references in drug panel contains PUBMED prefix (#666) * Small improvement: list of projects is auto refreshed every 5 seconds if at least one of the project is uploading/removing (#610) * Small improvement: passwords to email account and ldap are not sent over API (#732) * Small improvement: reactant/product/modifier specific colors are parsed properly from CellDesigner file (#597) * Small improvement: Info tab contains information about disease and organism when info is provided * Small improvement: Info tab provides information about model annotations and submap tabs provide information about submaps annotations if applicable (#591) * Small improvement: uploading sbml file should automatically discover a file type (#784) * Small improvement: when plugin listeners crash the system notifies user about problem with a plugin (#767) * Small improvement: when exporting reaction and elements there is possibility to filter by (sub)map (#615) * Small improvement: during first opening of a map, the zoom level is automatically computed if no default information is provided (#776) * Small improvement: when adding new project columns "Root map", "Mapping file" and "Map type" are merged (#700) * Small improvement: allow admin to disable CORS check (#802) * Small improvement: TransparencyZoomLevelVisibility parameter renamed to SemanticZoomLevelTransparency (#801) * Small improvement: export/import from SBML support z-index in LAYOUT extension * Bug fix: due to blocking of our requests from ctdbase the autocomplete for this database is disabled * Bug fix: deprecated columns in data overlay are not visible to the end user (#827) * Bug fix: invalid color in data overlay provides proper feedback to the user (#822) * Bug fix: genetic variant overlay without name caused problems (#832) * Bug fix: tair locus identifiers were used improperly - instead of id the name was used * Bug fix: plugin tab header wasn't properly resized after adding plugins that introduced second line for tab selection (#758) * Bug fix: invisible layer shouldn't be shown on the map (#813) * Bug fix: list of availbale annotators is sorted alphabetically (#815) * Bug fix: redirect url from export panel is fixed (#819) * Bug fix: allow to reupload the same file without closing add overlay dialog (#833) * Bug fix: gene_name column is allowed only in the genetic variant data overlay * Bug fix: protein types are sorted properly in "Select valid annotations" dialog (#815) * Bug fix: if there is a description of (sub)map then it is available in info/submap panel (#824) * Bug fix: empty type for data overlay is allowed (#827) * Bug fix: genetic variants data overlay was ignoring color parameter (#827) * Bug fix: asynchronous calls on showing/hiding data overlays might cause problems due to network latency (#830) * Bug fix: progress bar of gene genome mapping upload is refreshing properly (#728) * Bug fix: when editing project Disease and Organism could not be removed (#616) * Bug fix: dashed line partially wasn't dashed in "Unknown Catalysis" and "Unknown Inhibition" reactions (#664) * Bug fix: "Unknown Catalysis" and "Unknown Inhibition" reaction end is slightly separated from target phenotype (#664) * Bug fix: order of genomes in admin panel doesn't change after refreshing list of genomes (#761) * Bug fix: fixing situation when Molart started with variation overlay not having the aa change information * Bug fix: plugin contect element width is adjusted when link to tabs are wrapped in more than one line (#758) * Bug fix: export to CellDesigner preserve font size (#798) * Bug fix: layout data was ignored for some reactions when importing from SBML (#812) -- Piotr Gawron Thu, 27 Jun 2019 14:00:00 +0200 minerva (13.0.0) stable; urgency=medium * Bug fix: Since Oracle Java cannot be installed as debian dependency we use openjdk-8. Due to this dependency minerva can be no longer installed on Ubuntu-14 (#223) -- Piotr Gawron Mon, 6 May 2019 18:00:00 +0200 minerva (12.2.3) stable; urgency=medium * Bug fix: sorting of entries in "Edit project->overlays" dialog fixed (#790) * Bug fix: searching of chemicals stopped working due to expired SSL certificate on https://ctdbase.org/ * Bug fix: remove button is disabled after starting removing of the data overlay (#791) * Bug fix: search autocomplete hint could be initially hidden (#793) * Bug fix: updating terms of use could crash when list of users was removed in separate tab or by another user (#797) * Bug fix: name of the checkbox in ADD PROJECT window adjusted (#799) * Bug fix: when user didn't have privileges to remove comments the button was active on pages other than page 1 (#792) * Bug fix: export of reaction to SBML didn't work when lines on the map were too short (#805) -- Piotr Gawron Wed, 24 Apr 2019 17:00:00 +0200 minerva (12.2.2) stable; urgency=medium * Bug fix: downloading overlays didn't work from admin panel when project with different id than default map was accessed * Bug fix: change of owner of the data overlay in admin panel incorrectly ordered overlays (#777) * Bug fix: chemical search didn't use updated disease identifier, original disease id from project upload was used instead (#779) * Bug fix: user login with special characters (like '@') could cause problems in admin panel (#780) * Bug fix: removing project without full control in the system (but with enough privileges to remove project) caused "Not enough privileges" error (#778) * Bug fix: export of custom properties (like synonyms) are properly encoded in CellDesigner xml (#785) * Bug fix: notification about not supported version in IE 11 fixed (#783) -- Piotr Gawron Tue, 9 Apr 2019 17:00:00 +0200 minerva (12.2.1) stable; urgency=medium * Bug fix: export of reaction colorsi in SBML is properly encoded (COPASI can read colors properly) (#744) * Bug fix: removing active plugin didn't switch plugin tab to the next loaded plugin (#757) * Bug fix: closed submap will not be reopened after page refresh (#763) * Bug fix: comment remove button is disabled for users without proper privileges (#766) * Bug fix: invalid pubmed identifier could break clicking on element containing it (#764, #765, #769) * Bug fix: cache for API queries is explicitly disabled - some queries could be mistakenly cached and the system behaviour might get unstable (#771) -- Piotr Gawron Mon, 1 Apr 2019 17:00:00 +0200 minerva (12.2.0) stable; urgency=medium * Feature: bug report utility * Feature: url GET parameters support all kind of search and selected overlays highlight * Feature: user can create custom logging configuration in file /etc/minerva/log4j.properties * Feature: plugin panel in admin allows to configure set of available plugins * Feature: import export from SBML supports RENDER package * Feature: import export from SBML supports MULTI package * Feature: API tool providing possibility to transform different types of file formats * Feature: current state of the browsed map is reflected in the url (position, zoom, overlays, search queries, etc.) * Small improvement: highlighting table rows in admin panel uses better contrast color (#706) * Small improvement: list of publication can be filtered by submap (#614) * Small improvement: size of add overlay window adjusted to show more data without scrollbars (#657) * Small improvement: all popup dialogs in the application have dialog specific css class names (#665) * Small improvement: JS plugin can create listener that is triggered on search results focus change * Small improvement: export to SBML includes unit factors * Small improvement: mesh identifiers are resolved to meshb.nlm.nih.gov urls * Small improvement: genetics information allows to provide information about modification on peptide level that could be visualized in MolArt * Small improvement: allow to control the background and font color of areas drawn from text areas in CellDesigner "layers" * Small improvement: config logo location is relative to the root minerva deployment directory * Small improvement: there is branding minerva logo in the left panel * Small improvement: there is possibility to download part of the map limited to set of reactions/elements * Small improvement: allow admin to configure parameters displayed in the left panel * Small improvement: arrows for Transcription Starting Sites looks more like in CellDesigner * Small improvement: popup window appear with info about exceeding max number of search results when necessary * Small improvement: plugins can define default width of the container tab * Small improvement: new miriam type is handled: ClinicalTrials.gov * Small improvement: click on the border of compartment select the compartment * Small improvement: there is max size of the map in configuration panel that disables upload of too big files * Small improvement: hitting enter on login page logs in the user (no need to click on the login button) * Small improvement: refresh button in overlays panel (useful when data overlays are uploaded separately in using API calls) * Small improvement: list of publications is downloadable * Small improvement: export of reactions support filtering by reaction type * Small improvement: 'BACK TO MAP' link is available only when guest account has proper access level * Small improvement: 'REQUEST AN ACCOUNT' link is available only the contact email account is provided * Small improvement: Plugin API allows to show/hide data overlays * Bug fix: Icons were sometimes not properly loaded on Safari (#661) * Bug fix: migration scripts are compatibile with postgres 9.3 version that is default on Ubuntu 14 (#762) * Bug fix: update/remove button is disabled when user has no privileges for managing overlays (#742) * Bug fix: when user cannot manage users information in overlays and users tab in edit project dialog is provided instead of hiding tabs (#756) * Bug fix: removing comments in a project asked for confirmation twice after edit project dialog for specific project was opened; closed and opened again (#697) * Bug fix: editing/removing project requires Map Management privilege (#681) * Bug fix: when removeAllListeners is called list of registered listeners is cleaned (#687) * Bug fix: when plugin is removed the html elements associated with it are removed as well (#686) * Bug fix: when creating new user default privileges are set properly (#692) * Bug fix: plugin can be added after plugin has been removed in admin plugin panel (#686) * Bug fix: too many annotations (>=100) caused misaligning in the left panel (#708) * Bug fix: export to svg contains viewBox info (#716) * Bug fix: overlays added via API couldn't be visualized after refresh (#718) * Bug fix: Safari sometimes cached server responses and used wrong data, for example in admin panel configuration tab (#719) * Bug fix: description of transcription site is centered (#720) * Bug fix: selecting too few parameters in export doesn't throw reportable error (#721) * Bug fix: providing invalid overlay id in url could break minerva (#726) * Bug fix: removing project that doesn't exist doesn't cause 500 error (#723) * Bug fix: opening map with invalid id shows proper error message (#724) * Bug fix: Fixing an issue where search panel was not properly resized on expansion (#682) * Bug fix: loading icon is not overlapping input in the search panel (#404) * Bug fix: position of transcription sites in genes are computed properly (#553) * Bug fix: REQUEST AN ACCOUNT was enabled when associated email was invalid (#626) * Bug fix: working with too many maps within the single session could crash connection to server (#651) * Bug fix: drawing corrupted heterodimer association in CellDesigner could crash map upload (#673) * Bug fix: export to CellDesigner align inhibition reaction properly * Bug fix: export/import to/from SBML handles Heterodimer Association reaction properly * Bug fix: logo doesn't need to be square * Bug fix: when clicking on a search link (in overview window), input in the left tab was not modified * Bug fix: in admin panel changing of genome version is blocking interface until data about url is retrieved * Bug fix: export of species inside complex into CellDesigner was causing problems when reading the file in CellDesigner * Bug fix: export to SBGN did not export compartments * Bug fix: export of complex states to SBGN did not work * Bug fix: type of the data overlay can be defined in the file content (useful when uploading genetic variants) * Bug fix: CLEAR button clears comment checkbox if necessary * Bug fix: minerva install problem on ubuntu 18 fixed -- Piotr Gawron Mon, 25 Mar 2019 17:00:00 +0200 minerva (12.1.8) stable; urgency=medium * Bug fix: add a project reset users custom overlays limit to default (#679) * Bug fix: edit/remove project button was disabled based on Configuration Manage Privilege, but should be based on Project Manage Privilege (#681) * Bug fix: another minor problem with updating privileges introduced in 12.1.6 fixed (#659) -- Piotr Gawron Fri, 8 Feb 2019 15:30:00 +0200 minerva (12.1.7) stable; urgency=medium * Bug fix: problems with updating privileges introduced in 12.1.6 fixed -- Piotr Gawron Wed, 6 Feb 2019 15:30:00 +0200 minerva (12.1.6) stable; urgency=medium * Bug fix: logo on login page was broken with image link being full url * Bug fix: plugin API had sometimes problems with fetching reactions properly * Bug fix: upload of data overlays without privileges triggers proper error message also in situation when user cannot create projects * Bug fix: first login on website when there is Term of use to accept raised error for regular users * Bug fix: fetching some drugs via API could cause 500 -- Piotr Gawron Mon, 28 Jan 2019 16:00:00 +0200 minerva (12.1.5) stable; urgency=medium * Bug fix: Drugbank changed output format which crashed drug connector * Bug fix: word wrapping fixed in overlay table for long overlay names in Firefox browser -- Piotr Gawron Thu, 10 Jan 2019 14:00:00 +0200 minerva (12.1.4) stable; urgency=medium * Bug fix: no check for limit on custom data overlays fixed * Bug fix: error message improved when there is privilege problem during data overlay upload * Bug fix: upload of data overlay from admin panel didn't work * Bug fix: add project button is disabled when user doesn't have proper privileges ("Add project" privilege) * Bug fix: there are no more extra markers due to map wrapping * Bug fix: upload of the project failed when another project was removed during upload * Bug fix: word wrapping fixed in overlay table for long overlay names -- Piotr Gawron Fri, 28 Dec 2018 14:00:00 +0200 minerva (12.1.3) stable; urgency=medium * Bug fix: add project button is disabled when user has no privileges * Bug fix: projectId was missing in the edit window * Bug fix: user could provide invalid mesh ID that caused errors when browsing map * Bug fix: user created from LDAP connection doesn't have a password stored in the database -- Piotr Gawron Fri, 14 Dec 2018 14:00:00 +0200 minerva (12.1.2) stable; urgency=medium * Bug fix: vmh annotations should be properly matching id entered in the input * Bug fix: opacity was not working when highliting objects in plugins * Bug fix: integer configurtion options (like SMTP_PORT) are properly validated before saving * Bug fix: inside of reaction box wasn't properly aligned * Bug fix: too long data overlay name disturbed size of the map div and interaction with the map * Bug fix: search for some drugs resulted in internal server error * Bug fix: LDAP login is case insensitive * Bug fix: adding user could end up with error in the frontend -- Piotr Gawron Wed, 12 Dec 2018 16:00:00 +0200 minerva (12.1.1) stable; urgency=medium * Bug fix: lineWidth in data overlays was ignored * Bug fix: legend was blinking after using controls * Bug fix: comment header was missing * Bug fix: click on drug target zooms to the results * Bug fix: export columns return proper value types * Bug fix: partial zooming is disabled -- Piotr Gawron Fri, 2 Nov 2018 13:00:00 +0200 minerva (12.1.0) stable; urgency=medium * Small improvement: default privilege value for 'Custom overlays' added * Small improvement: explicit logging of successful and unsuccessful logins * Small improvement: clicking on search result icon (on the map) change tab to the corresponding search results * Small improvement: option to remove additional overlays generated by custom semantic zoom * Small improvement: 'Reduced modulation' edge was displayed differently in CellDesigner and Minerva * Small improvement: user-friendly documentation for plugin URL field * Small improvement: plugins have to access information about active submap * Feature: genome browser with gene variants * Feature: support of all CellDesigner element modifications * Feature: ldap authentication * Feature: multicolored anchors for data overlays * Feature: minerva is distributed using rpm packages * Small improvement: annotations from RHEA are handled * Small improvement: changing of Terms of Service url allows admin to reset the status of ToS acceptance for all users * Small improvement: description of a grouped results in improved * Small improvement: selection of required annotation on map upload improved * Bug fix: annotations for elements with mutation in name (like "BID (p15)") weren't provided properly * Bug fix: passwords in the configuration tab are hidden with '*' * Bug fix: user has access to transparency level when creating custom semantic view (without this parametere functionality was very difficult to use) * Bug fix: loading invalid plugin doesn't render empty div anymore * Bug fix: sorting of custom overlays was broken when description of overlay was present * Bug fix: when there is a problem with adjusting font in complexes (because the font should be smaller than 1pt) description is not drawn anymore * Bug fix: going to export page and back was breaking a map * Bug fix: coordinates of selected area wasn't processed properly when they exceeded canvas * Bug fix: postgres migration script fixed to work with new docker compose * Bug fix: double click on user add button disabled * Bug fix: privileges are mirrored correctly across different popups * Bug fix: plugin tab css fixed * Bug fix: uploading sbml file with no ids in glyphs returned error that could not be easily understand * Bug fix: ds_store files in subfolders crashed zip upload * Bug fix: when creating new user default privileges were not filled -- Piotr Gawron Mon, 29 Oct 2018 13:00:00 +0200 minerva (12.0.4) stable; urgency=medium * Bug fix: CellDesigner modifications that are drawn as reaction are handled properly (like catalysis) * Bug fix: Removing of guest (anonymous) account is forbidden - system is unstable after removing such user * Bug fix: Tair database moved to https * Bug fix: Taxnomy database changed html output that resulted in problems with resolving species name to the id -- Piotr Gawron Wed, 12 Sep 2018 17:00:00 +0200 minerva (12.0.3) stable; urgency=medium * Bug fix: SBML model annotations caused errors on upload * Bug fix: Export of some models to SBML didn't work properly * Bug fix: zip files weren't processed properly * Bug fix: required annotations were always required for some types * Bug fix: user cannot remove default map anymore -- Piotr Gawron Mon, 27 Aug 2018 11:00:00 +0200 minerva (12.0.2) stable; urgency=medium * Bug fix: data overlay by annotation type fixed * Bug fix: [plugin] getting reactions with set of id larger than 100 elements works properly * Bug fix: name of commented protein was remembered for the new comment * Bug fix: setting zoom level wasn't ranged and validated * Bug fix: when uploading data overlay there is a warning regarding mixed new line characters when necessary * Performance: tomcat inside docker image by default can use 3G of memory -- Piotr Gawron Tue, 31 Jul 2018 13:00:00 +0200 minerva (12.0.1) stable; urgency=medium * Bug fix: setting default zoom level on submap * Bug fix: opened submap had different background then current selection * Bug fix: clicking on comments was difficult in OpenLayers * Bug fix: general map comment didn't display coordinates properly * Bug fix: opening map could crash when CellDesigner file contained duplicate reaction id * Bug fix: map is repositioned when info window is outside of current view in OpenLayers library -- Piotr Gawron Tue, 24 Jul 2018 10:00:00 +0200 minerva (12.0.0) stable; urgency=medium * Feature: There is alternative OpenLayers map engine available * Feature: database connection configuration (login, password, host, etc) can be modified using /etc/minerva/db.properties file * Feature: searching for elements in submap gives marker on top map indicating the submap connection * Feature: similar search results are merged * Feature: visualization of protein structures by MolArt * Feature: reordering of data overlays is supported * Feature: support for STRING, STITCH, KEGG, CAZy, BRENDA annotators * Feature: annotations contain info about source (there is difference between manual and automatically added annotations) * Feature: default permission for new projects are configurable * Feature: SBML support (with and without layout extension) * Feature: kinetics support * Feature: plugin API * Feature: all functionalities are provided via REST API * Feature: visualization of two (or more) overlaying results (like drug target, mirna target) is highlighted with different icon * Small improvement: email for account request contain configurable text * Small improvement: transparency level for data overlays is configurable * Small improvement: CellDesigner reactions of Modifier type are acceptable * Small improvement: performance improved for overlays identified by annotation identifiers * Small improvement: Legend is always on top * Small improvement: When email content is too big it's compressed * Small improvement: Description of chemical panel refers to the disease connected to the map * Small improvement: Confirm button when removing data overlay * Small improvement: Clicking on data overlayed element behaves in the same way as clicking on not overlayed element * Small improvement: Title of list of submaps doesn't contain UNKNOWN tag * Small improvement: DOI is supported as miriam type * Small improvement: When loading data in search tab there is "LOADING" icon * Small improvement: Data overlays can use source element identifiers for filtering * Small improvement: Data overlays can submap column to differentiate between maps * Small improvement: search by chemical names is possible * Small improvement: auto complete functionality for drugs, mirnas and chemicals * Small improvement: columns value and type are not mutually exclusive in data overlays * Small improvement: column type is case insensitive in data overlays * Small improvement: every submap contains default center position and zoom level to customize default view when entering map for the first time * Small improvement: data overlays color scale contains configurable default middle color (for 0 values) * Small improvement: opening data overlay switch to empty background * Small improvement: multiple x-frame domains are allowed * Small improvement: No duration of the text notification in overlay tab * Small improvement: JS plugin API allows to store data on server side * Small improvement: submap reference in publication list * Small improvement: size of connection to database reduced to 90 (so default connection pool to postgres is not completely filled with minerva) * Small improvement: visualization of sbml function improved (lambda expression removed from the definition) * Small improvement: handling of additional miriam types from BiGG ontology * Small improvement: configuration options are grouped in categories * Bug fix: searching with two queries sometimes resulted in one complex instead of two queries * Bug fix: uploaded submaps didn't have hierarchical masking * Bug fix: uploading of zip files created by mac doesn't crash due to .DS_Store folder * Bug fix: auto complete is case insensitive * Bug fix: google maps API 404 errors for non existing tiles are removed -- Piotr Gawron Mon, 16 Jul 2018 12:00:00 +0200 minerva (11.1.3) stable; urgency=medium * Bug fix RPM: remove directory with contents of unpacked war file when uninstalling * Bug fix: don't append Google API key to Google maps javascript URL when it is not set -- Piotr Gawron Mon, 23 Jul 2018 12:00:00 +0200 minerva (11.1.2) stable; urgency=medium * Bug fix: Searching for chemicals with invalid mesh ID crashed * Bug fix: opening map that was removed and re-uploaded could crash * warning message due to lack of google consent improved -- Piotr Gawron Wed, 04 Jul 2018 16:00:00 +0200 minerva (11.1.1) stable; urgency=medium * Bug fix: Updating privileges takes much less time * Bug fix: Concurent update on privileges shouldn't crash anymore * Bug fix: Search by element id crashed when submaps were available * Bug fix: GO connector uses new API, because the old one was turned off and stopped working -- Piotr Gawron Wed, 27 Jun 2018 15:00:00 +0200 minerva (11.1.0) stable; urgency=high * User can provide Google Maps API key that must be registered in google cloud account * User data overlays must be Google Maps API terms of use compliant * Terms of Use added -- Piotr Gawron Tue, 05 Jun 2018 9:00:00 +0200 minerva (11.0.10) stable; urgency=medium * Bug fix: link from overview image to search result was broken -- Piotr Gawron Wed, 16 Apr 2018 15:00:00 +0200 minerva (11.0.9) stable; urgency=medium * Bug fix: some comment couldn't be loaded * Bug fix: when adding comment it didn't appear on map immediately -- Piotr Gawron Wed, 21 Feb 2018 18:00:00 +0200 minerva (11.0.8) stable; urgency=medium * Bug fix: XSS vulnerability * Bug fix: "java.lang.IllegalStateException: getWriter()" exceptions in logs * Bug fix: crash for uploading and caching chemical data * Bug fix: disappearing tiles in submodels * Bug fix: max number of results is properly taken from configuration * Bug fix: overlay cannot be hidden before process of fetching data during opening is finished * Bug fix: redirection to login page when session expired and access to export page is requested * Bug fix: sometimes overlays couldn't be hidden in submaps * Bug fix: comments on submaps are visualized properly -- Piotr Gawron Mon, 05 Feb 2018 18:00:00 +0200 minerva (11.0.7) stable; urgency=medium * Bug fix: redirection added when anonymous tries to access secured map * Bug fix: loading time of custom overlays is reduced * Bug fix: there should be no problem with symlink when upgrading debian package * Bug fix: number of services changed API address to https: pmceurope (pubmed), uniprot, ensembl, hgnc, recon, ctd database -- Piotr Gawron Thu, 18 Jan 2018 16:00:00 +0200 minerva (11.0.6) stable; urgency=medium * Bug fix: fix a bug when entering invalid mirna id -- Piotr Gawron Thu, 14 Dec 2017 16:00:00 +0200 minerva (11.0.5) stable; urgency=medium * Bug fix: fix on connection to drugbank database * Bug fix: posttranslational modification data was sometimes unavailable in search results panel -- Piotr Gawron Thu, 30 Nov 2017 16:00:00 +0200 minerva (11.0.4) stable; urgency=medium * Bug fix: fix on connection to taxonomy database * Bug fix: color coding for reactions (wrong color was chosen) * Bug fix: overlays with many reactions did not work properly -- Piotr Gawron Thu, 09 Nov 2017 14:50:00 +0200 minerva (11.0.3) stable; urgency=medium * Bug fix: removing empty project removed images from all projects * Bug fix: clicking on map when left panel was hidden threw error * Bug fix: links to invalid annotations were opening invalid web page * Bug fix: service resolving miriam resources doesn't work over http anymore * Bug fix: chebi annotator doesn't work over http anymore -- Piotr Gawron Thu, 19 Oct 2017 13:50:00 +0200 minerva (11.0.2) stable; urgency=medium * Bug fix: login issues when default page is in secure area -- Piotr Gawron Fri, 25 Sep 2017 12:00:00 +0200 minerva (11.0.1) stable; urgency=medium * Bug fix: logout caused issues with session data -- Piotr Gawron Fri, 08 Sep 2017 12:00:00 +0200 minerva (11.0.0) stable; urgency=medium * Bug fix: security issue - access to specific map can be restricted by the user login * Bug fix: sbgn import * Bug fix: mesh connector * Rest API (documentation can be found here: https://git-r3lab.uni.lu/piotr.gawron/minerva/blob/master/README.md) * Selecting an element on the map shows info about it in the bottom left corner (when Search tab is not open) * Upload of data overlays allows to upload just names of the proteins (or other elements), it can be done via file or just by typing in the proper text box * Layout changes: the main one is that there are only 3 tab panels (search, overlay, info), so it should be easier to navigate -- Piotr Gawron Mon, 28 Aug 2017 12:00:00 +0200 minerva (10.0.5) stable; urgency=medium * Bug fix: interacting drugs can be found for RNAs * Bug fix: error handling improved on map upload * Bug fix: taxonomy ncbi server switched to https * Overlay presents description field if possible -- Piotr Gawron Sat, 04 Mar 2017 12:00:00 +0200 minerva (10.0.4) stable; urgency=medium * Bug fix: overlays colors are centered in white (not black) * Bug fix: export to CellDesigner fixed * Bug fix: DrugBank connector updated due to change in DrugBank website -- Piotr Gawron Thu, 29 Dec 2016 17:01:16 +0200 minerva (10.0.3) stable; urgency=medium * Bug fix: login cannot contain whitespace * Bug fix: search for multiple drugs will not return more drugs than queried for * Bug fix: drug list for some proteins (like RHOA) hung webpage * Bug fix: comments on submaps issue * Bug fix: link to submap from comment panel * Overlay coloring can be defined in Configuration -- Piotr Gawron Thu, 15 Dec 2016 15:01:16 +0200 minerva (10.0.2) stable; urgency=medium * Bug fix: markers for mirna targets visibility -- Piotr Gawron Thu, 29 Sep 2016 10:01:16 +0200 minerva (10.0.1) stable; urgency=medium * Bug fix: export to image * Bug fix: trigger reaction and physical stimulation reactions are no longer allowed (CellDesigner data model issue) * Bug fix: clicking on reactions in submaps -- Piotr Gawron Fri, 21 Sep 2016 13:01:16 +0200 minerva (10) stable; urgency=medium * Project info tab available for users * Management of overlays in admin panel * Bug fix: Visualization of text mining * Bug fix: Exception when accessing non-existing project * Bug fix: Zooming issue when searching for results on submaps * Bug fix: Out of memory when caching a lot of data * Bug fix: Corrupted drug names * Bug fix: Unexpected errors when uploading layouts * Bug fix: Coordinates in url * Bug fix: Hiding left panel * Bug fix: CellDesigner font size is processed properly * Bug fix: Search by reaction id is not case sensitive -- Piotr Gawron Mon, 22 Aug 2016 13:01:16 +0200 minerva (9) stable; urgency=medium * Fix on install script of version 8 that crashed some new installations -- Piotr Gawron Wed, 29 Jun 2016 09:58:34 +0200 minerva (8) stable; urgency=medium * Micro RNA interface * Toxic chemicals interface * Data sets (layouts) visualized dynamically in the browser * Reverse query for drugs, chemicals, micro RNAs interfaces * Small bug fixes -- Piotr Gawron Thu, 14 Apr 2016 13:03:55 +0200 minerva (7) stable; urgency=low * Uploaded datasets are available for download * Entrez annotator * Ensembl annotator * Valid/required annotations and used annotations saved in user profile * Export to pdf/png/jpg/svg * New web interface -- Piotr Gawron Thu, 3 Dec 2015 22:00:00 +0200 minerva (6) stable; urgency=low * Searching by annotations * Errors from parsing data forwarded to client * Notification email system added * Warnings are downloadable * Complex map (composed from many small maps) * Visualization of Recon specific annotations * Versioning system * Galaxy connector * Miriam types report * Advanced annotation options * Uniprot annotation module * Customized validation of miriam annotations * Recon annotation service * Bug fix: Data autofill problem in user management * Bug fix: User privileges for adding project * Bug fix: Problem with some miriam entries in RDF format * Bug fix: Reporting of drawing problems * Bug fix: Visualization of posttranslationa modification * Bug fix: Drugbank problem after update of Drugbank interface * Bug fix: Session scope fixed (browsing many maps at the same time) * Bug fix: Asynchronous removing/adding maps * Bug fix: Export to CellDesigner rarely produced corrupted CellDesigner file * Bug fix: Recon annotations of reactions * Bug fix: Login problem when browsing not default map * Bug fix: Multimers are available for every element -- Piotr Gawron Tue, 21 Jul 2015 22:00:00 +0200 minerva (5) stable; urgency=low * Additional checkboxes in upload model: annotate automatically, cache data, verify annotations * Popup window in admin panel that list warnings * Information about build * Parsing and annotation warnings for models in admin panel * Custom reaction visualization in upload overlay * Bug fix: Problem with touch interface on Windows 8.1 * Bug fix: Google Maps API problem with floating bubbles * Bug fix: Error handling in admin panel * Bug fix: Reaction color in CellDesigner file * Bug fix: Reaction line width -- Piotr Gawron Thu, 18 Dec 2014 22:00:00 +0200 minerva (4) stable; urgency=low * Export of the part of the map into CellDesigner file * Logo files managable via config webpage * Import data from GO * Custom overlay upload * Additional structural information imported from annotation service * Bug fix: Fonts and lines in hierarchical view * Bug fix: Visualization of residues in rna, antisense rna, proteins * Bug fix: Problem with touching bubbles on touch interface * Bug fix: Problem with special UTF-8 characters in CellDesigner file * Bug fix: Problem with users and session expire * Bug fix: Export problem -- Piotr Gawron Thu, 11 Sep 2014 22:00:00 +0200 minerva (3) stable; urgency=low * Drug targeting interface * Export to CellDesigner * Status page of all dependent services * Configuration page -- Piotr Gawron Thu, 5 Jun 2014 22:00:00 +0200 minerva (2) stable; urgency=low * Upload of the CellDesigner map * Bug fix: Problem with touch interface after update of browsers engine * Bug fix: Problem in Safari when searching for elements -- Piotr Gawron Wed, 2 Apr 2014 22:00:00 +0200 minerva (1) stable; urgency=low * Initial release -- Piotr Gawron Wed, 4 Dec 2013 22:00:00 +0200